While, Barack Obama, may have good reasons to be angry with the reelected prime minister of Israel, he may have strained the line to a point where it might backlash on him, as explained in the linked, New York Times article.
My opinion on this subject is that the strained relationship between the US and Israel, are a result of similar ideological struggles within each side, and while it may seem like Obama is simply upset with Netanyahu teaming up with his political and ideological rivals, his concerns may go beyond that, into real implications on the future of the US.

It's really complicated, to be sure. I think no matter what the difference is, there's always something both personal and political in these kinds of relations. Surely there have been opponents who, because they are good friends, their ideological differences didnt' seem as great.